Filling in the Blanks
by VoteSaxon16
Summary: The Doctor wakes up in a mental hospital with no memory of how he got there. Amy is living in a painful alternate reality. Danger closes in, taking the form of the Doctor's oldest friend. It's a race against time as the Doctor must recover his memory, escape the hospital with Amy in tow, and avoid death yet again, without his TARDIS. If he fails...
1. Chapter 1

A/N This is my first fanfic, so reviews are much appreciated. I am sorry for the Nickelback reference. I'm so, so, sorry. But I could not resist.

The Doctor's eyes snapped open. He tried to sit up, but leather cuffs on his wrists and ankles prevented any useful movement. He wriggled a bit, the surface underneath him was soft and yielding, and the Doctor quickly deduced it was a bed. Why was he chained to a bed? He scanned his surroundings. Across from his bed sat a desk made of cheap laminate wood, bolted to the wall. To his left were windows, and a shelving unit beneath them. Closer inspection of the windows revealed that they were reinforced with metal netting, and were bolted shut. This was too nice for a prison, clearly, so where was he? Psych ward, possibly. To his right was another wall, with a red button near his bed, just out of his reach. Oooh, now they were just taunting him. The paper clothing he was wearing and incoherent shouts down the hall confirmed his suspicions: he was in a mental hospital. He could not remember how he had ended up here. Last thing he remembered, he was in the TARDIS with his Ponds. The TARDIS! His Ponds! Where were they? He took a breath to steady himself. He reached out with his mind; if the TARDIS was nearby he could link telepathically with her and gather more information. It was futile, however, wherever she was, it wasn't in this solar system. He hoped she was simply in the Vortex, preferably with the Ponds inside, safe. Why couldn't he remember how he ended up here?

A woman, presumably a nurse, entered his room, interrupting his thoughts. "Mr. Smith?" Apparently he was playing human. That meant one of two things: Either he was on Earth, relatively early in its timeline, or, wherever he was, revealing the truth was dangerous. Based on the nurse's outfit (flare jeans and a Nickelback T-shirt), and the Motorola Razr clipped to her belt loop, he guessed the former: probably sometime in the middle of the 2000s AD. What had happened to his memories? Clearly someone- or something- didn't want him remembering.

"Yes, that's me!', he said, finally, attempting to sound cheery so maybe he'd be let out of these stupid restraints. "And you are?"

"I'm Mallory Lupin, your nurse. I have some meds here you need to take."

"Meds? What meds?"

"Let me have a look at your chart…Perphenazine, Cogentin, and Ritalin, looks like."

"I don't want them'

"You don't have to take them, but I can't let you out of those restraints until you do."

Well, he wasn't about to lie here all day, when he needed to find his Ponds. The effects of the pills would not be pleasant, but he could work though them."Alright, I guess I will take them, then"

"Now we're talking", Mallory said, smiling as she unlocked each of his hands so he could sit. The doctor assumed she would not free him completely until he took the pills. Mallory handed him a paper cup containing the pills, and a small water bottle. Reluctantly, he placed the pills on his tongue, took a swig of water, and swallowed the pills. After checking under his tongue to ensure he had actually swallowed the pills, Mallory undid the cuffs on his ankles.

"Wait here a minute and I will go get your clothes from the nurses' station", Mallory instructed. She left the room and returned with a paper bag containing his trousers, shirt, and tweed jacket. His suspenders, bow tie, and shoes were predictably, absent. Suicide risk for the two former, elopement risk for the latter, the Doctor thought grimly.

"There is a toothbrush, toothpaste, and a comb in the bathroom", Mallory said, pointing to a closed door near the door that led to the hall. "Get dressed and cleaned up, then please head to the common room at the end of the hall." Mallory left the room. The Doctor happily shed the paper clothing and relished the familiarity of his own clothing. He brushed his teeth and quickly combed through his floppy, brown mess of hair. He left his room and found his way to the "common room". People sat at tables or lounged on couches. A few were conversing, but most either stared blankly at the cracked television or simply slept, due to heavy medication, no doubt. At a table, sitting by herself, however was a familiar redhead. Her eyes met his. Her eyes widened in recognition…then fear? But why would Amy be afraid of him? Why was she here? More important, how long had she been here? What had they done to make her fear him? Had he come here intentionally, to rescue Amy? No, that didn't make sense; they wouldn't have cuffed him to the bed if he didn't put up a fight. Why was he here? Why was Amy here? What was tampering with his memory? The Doctor wanted answers, and he would do anything it took to get them.


	2. Chapter 2

A/N Spoilers (sweetie) up to the Pandorica Opens/The Big Bang plus mentions of the Silence.

The Doctor's first priority was Amy. He had to know the reason behind her reaction. So, logically, he strode over to where she sat and pulled up a chair. She regarded him with wary eyes.

"Hello, Amy"

"H-How do you know my name?"

"Amy, it's me, The Doctor. Amy, please tell me you remember!"

She reached out to touch his face. In awe, she ran her hand down his jaw, tracing his chin. "You're real. How are you real?!" Amy blinked back tears.

"Of course I'm real. Don't you remember? We traveled the stars, you and me- and Rory, too. Please tell me you remember."

"The doctors said you weren't real. They shoved me full of dreadful medication and when I still insisted you were real, they locked me away here! I've been here for two years, Raggedy Doctor. I lost two years of my life because of you! I've spent my whole life suffering for a madman in his blue box who promised me 5 minutes but never came back! And now you are here- fifteen years and a living hell too late!"

That put them in the year 2011. Apparently, his nurse was a bit behind the times, the Doctor thought absently. He sighed, and placed Amy's hands in his. She flinched, but did not pull away. "Oh, Amy, he murmured. This was not supposed to happen. None of this was supposed to happen. We saved the Starship UK. We survived the Weeping Angels at the Byzantium crash. We met Winston Churchill and you flirted with Vincent Van Gogh. You were trapped in the Pandorica, and Rory waited 2,000 years for you, you know. He was known as The Last Centurion. But the universe was dying, so I sacrificed myself bringing it back, but you saved me. All you had to do was remember, and there I was, at your wedding. And something went very, very wrong. Something altered the timeline. And here, now, all you've done is suffer, isn't it?"

The tears flowed freely now, and Amy nodded. She allowed her Raggedy Doctor to pull her into an embrace, her head resting on his shoulders. Unfortunately, this garnered the attention of a nurse, who bustled over and chastised the Doctor "Mr. Smith"; she called him, for his lack of boundaries.

Reluctantly, the Doctor pulled away from Amy. He looked at her sadly. "I will fix this, I promise. You will not have to suffer any more if I have anything to do with it. Now, my memory has been tampered with. I don't know how I ended up here. Last thing I remember, I was traveling with you! So, what do you know about how I got here?"

"I don't know much, but I will tell you what I do know. You came in last night, screaming. 'The Silence are everywhere', whatever that means. You were covered in tally marks." The nurses drugged you up, hosed you down, and took you into your room. And, judging by the state of your wrists, they restrained you."

The Doctor frowned. "The Silence" sounded very familiar, but he couldn't place how. Most troubling was the fact that nothing Amy said jogged his memory. Just then, a burly male nurse with an impressively long beard informed the patients that it was time to line up to go to the cafeteria for lunch.

"We aren't elementary students", the Doctor complained to Amy, indignant.

"That's hardly the worst part of lunch"' she smirked. "The food is revolting!"

The Doctor allowed himself a small smile. Despite what Amy had gone through, despite whatever was tampering with his memory, here they were, making jokes. They stood near the back of the godforsaken line, which began to move forward, out of the building.

The cafeteria smelled of rotten eggs. Amy grabbed a tray, and allowed the attendants to pile gross-looking food onto it. The Doctor followed suit. Amy retrieved a paper cup and headed over to the soda machine, filling it with Diet Coke. At least the place had a soda machine. The Doctor was ecstatic to see that they had orange soda. The idea of soda with orange flavor was almost as amazing as beds with ladders! He sat down with Amy at a vacant table far from the nurses. He hoped the food wasn't too horrid today, because he was unusually ravenous, most likely from the perphenazine he had been forced to ingest. Unfortunately, it was inedible. Amy agreed, so they made do with their sodas.

"I have to ask, what is your real name? It's not Raggedy Doctor, obviously, and the nurse called you Mr. Smith"

"I'm a Time Lord, an alien, the last of my kind. Time Lords only reveal their names to their spouses, so we called each other by titles instead. I go by the Doctor, still. I call myself John Smith, when I need to pass as human."

"You're an alien? You look human enough to me, aside from that chin. I would expect an alien to look a bit more…Exotic.

"Actually, you look Time Lord. We came first."

"So, Doctor, you told me we did all these impossible things, traveling through time and space. If all those things really happened, how have I been here for two years?"

"I'm still trying to figure that part out. Though whatever it is, it created and is sustaining this paradox. In other words, it's very bad and very powerful."


	3. Chapter 3

**A/N**: I planned to update sooner, but preparing for a new school (and school year, for that matter) has been a real drain on my time. I hope to be able to update frequently and regularly once school begins and I get into some sort of routine. That said, this chapter will be very brief due to aforementioned time constraints. The Master shows up, though! :)

**WARNING: Spoilers for series 6 **

That face. The Doctor knew that face. Devious grin, slight stubble, white-blond hair. The Master. But how? This was impossible!

"Amnesia, Doctor? Oh you, poor, poor thing!", the Master crooned mockingly. "Can you hear them now, Doctor?"

"No more than I ever have, old friend." The Doctor looked around. A woman, wearing a metal eyepatch and a mirthless smile stood off to the side. He knew he had seen her before.

"I see you have noticed my little accomplice, Doctor. Madame Kovarian, she calls herself. Se is the leader of a religious order called the Silence, whose ultimate goal is your destruction. You know, I'm not typically religious, but consider me converted!" Another malicious smile lit up the Master's face.

"Well, I'm here and unarmed, as usual. Why haven't you killed me yet?"

"Oh, Doctor. We hardly have you captured. You are dreaming. But Madame Kovarian here has technology to rival the Time Lords. This is merely a psychic link. But don't worry! It's only a matter of time until we find you!" The Master laughed mirthlessly.

The Doctor woke up screaming. A nurse rushed into his room, concerned.

"No need to worry, just a nightmare."

"Oh, alright. Let me know if you need anything, Mr. Smith."

**A/N**: Like I said, brief. Reviews are appreciated, and thanks for your patience!


	4. Chapter 4

**A/N** Okay, finally! A nice, long(ish) chapter! Enjoy :)

The Doctor did not resume his sleep. He replayed the dream/message over and over in his mind, looking for information he may have missed. Then something hit him:

_"So, Doctor, you told me we did all these impossible things, traveling through time and space. If all those things really happened, how have I been here two years?"_

_"I'm still trying to figure that part out. Though whatever it is, it created and is sustaining this paradox. In other words, it's very bad and very powerful."_

His missing TARDIS. The Master. The Master had made another Paradox Machine.

Then something else: The Silence. He remembered! This was very bad. If they wanted to prevent him unleashing hell on the Universe, then surely they would never tolerate the Master's schemes. They were using the Master as a puppet to get to him! After that, however, the Doctor predicted a very short, painful future for the Master. His oldest friend-turned enemy was in danger.

**DWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDW**

The Doctor blinked back tears, afraid for both his TARDIS and his old friend. The TARDIS was surely in pain, and if this Kovarian woman found out who the Master really was, he might lose him again, maybe permanently.

Light slowly filled the sky outside his window. Too soon, Mallory unlocked his door and entered, holding the dreaded pill cup and water bottle. At least no one was trying to give him aspirin. He tried his best to appear cheerful.

"Good morning, Mallory! How are the, erm, nurse duties going?"

"Good morning, Mr. Smith. Quite well, actually. How about you? Are you feeling any better today?"

The Doctor was not feeling well at all, between the effects of the pills and the message he had received a few hours ago, but, knowing a good answer could get him out of here more quickly than he could escape sans his screwdriver, he lied. "Oh, I am feeling much better, thank you."

"No hallucinations?"

"Hallucinations?"

"When you arrived here you said you were a time traveling 'Time Lord of the planet Gallifrey', and that other aliens were chasing you."

Something had been chasing him? He filed that bit of information away, and replied "Nope. Human as they come, I am."

"Well, the records we received about you indicate no prior mental illness, and as your delusions no longer seem to be present, I would assume it was just short-lived psychosis. Surprisingly common, especially among individuals under a lot of stress. You will have to talk to our psychiatrist, Dr. Oswin, but I suspect you will be out of here within the next four days. At any rate, get down to the common room in the next ten minutes." She turned and left.

The Doctor felt a little better, knowing that, if no escape opportunities presented themselves, his stay here would be quite brief. The only remaining problem regarding his departure was how he would manage to get Amy out. He didn't need her to help defeat Kovarian and get the Master contained. Also, this version of her would be erased completely once he reversed the paradox. Still, pointless as it was, there was no way in hell he was leaving her after all she'd had to endure.

**DWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDWDW**

The Doctor made his way down to the common room. Breakfast wasn't for another fifteen minutes, so he sat down with Amy and proceeded to explain the situation.

"So, essentially, what you're telling me is the entire world, including me, was forced to live as slaves under your psychotic friend's reign of terror, while all the while he was torturing you. And no one has any recollection of this."

"Well, yeah. Pretty much."

"And you want to save him so he can travel with us? Well, you, and a me that never ended up here."

"I know it sounds insane, and honestly, it might be. But none of that was his doing. You see, my people, the Time Lords, made him the way he is. Ruthless, bloodthirsty, and mad. He hasn't been able to think for himself since we were kids. We were best friends, back then. I have to hold on to the hope that I can make him better. It's just us, now. He's the only one I've got."

"What do you mean?"

"Amy, my people were screaming, dying. So much death. The whole of creation, in danger. There was only one way to save the universe and defeat the Daleks. And that was to kill them all. To destroy both Skaro, home of the Daleks, and- and Gallifrey. I killed my own people, Amy. We were the only survivors."

"I'm sorry. I wish I knew what to say. But I don't know you, Doctor. I shouldn't exist, and I know, once you fix whatever's going on, that I won't anymore. Did your version of me know what to say?"

"Not exactly. But traveling with her and Rory does more for me than words ever could. Does it bother you, though? Knowing that when all this is over, you won't exist?"

"It's for the best, I think. A different, happy version of me will be traveling through the stars. I can hardly deny her that."

"Thank you. You have no idea how much this will mean to her, and how much it means to me."

"This is no time to get all emotional, Raggedy Man. It's not like I have much to lose. So, do you have a plan?"

"Well, they say I am getting released in the next couple of days. They will give my sonic screwdriver and psychic paper back to me at that point, as they have no idea who I am. Once I have those, getting you out should be a piece of cake"

"What about after that? We're still trying to save your nutter friend, right? What's the plan after we're out?"

"My favorite plan: Come up with a plan!"

Amy rolled her eyes. Just then, old Beardy the nurse announced breakfast.

"Not the line again!"

"Oh, yes, Raggedy Man. The line."

They filed out of the building. The Doctor knew the only thing left to do was to behave like a perfect little patient, and hope the release process was quick.


	5. Chapter 5

A/N: Guess who sucks at updating! Guess! Anyway, here's a new chapter. Please review as I love feedback! Special thanks to Codename-Valkyrie, Meilodi, Musicfriendsharmony, Sci5Vax, dalekjenn, dancergirl829, dcdaniellerocks, elliellie1, korifamous, and thisdayandage for following this story.

The day was uneventful. The Doctor paced the common room, overcome with cabin fever. Amy sat at a table, drawing a detailed picture of a curly haired woman in heels. Sensing the Doctor's restlessness, Amy offered to play chess with him.

"No thanks, Amy. Both of us know I would win. After all, I am Mr. Clever".

"Oi!"

"Well, it's true!"

"Alright, then, what DO you want to do?"

"Well, I want to have fish fingers and custard with Abe Lincoln, ride pterodactyls with River, join a barbershop quartet, and make the fez the official hat of the Third Great and Bountiful Human Empire".

Amy rolled her eyes and returned to her drawing.

"Mr. Smith?", called a petite, brunette woman.

"Yes?"

"I'm Doctor Oswin, do you mind if we have a chat in my office?"

"Not at all", answered the Doctor.

DWDWDWDWDWDWDWDWDW

"Alright, here's your suspenders, shoes, bow tie, ID, and... Is this a pen?"

"Yes. Yes it is, indeed, a pen"

"Okay then, you are free to go".

"Great! Just one thing... AMY!"

A/N

Cliffhanger, because I am a bad person. Remember, vote Saxon!


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